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首页> 外文期刊>Applications in plant sciences. >A Strategy to Recover a High-Quality, Complete Plastid Sequence from Low-Coverage Whole-Genome Sequencing
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A Strategy to Recover a High-Quality, Complete Plastid Sequence from Low-Coverage Whole-Genome Sequencing

机译：从低覆盖率全基因组测序中恢复高质量，完整质体序列的策略

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Premise of the study: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. Methods: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. Results: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. Discussion: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought.
机译：研究的前提：我们使用从低覆盖率454 GS FLX / Roche全基因组测序获得的数据，开发了一种生物信息学策略来恢复和组装叶绿体基因组。方法：采用比较基因组学方法从乌拉圭水稻的杂草生物型中获得完整的叶绿体基因组。我们还应用了适当的过滤器来区分代表叶绿体和核基因组之间新的DNA转移事件的读段。结果：从一组295,159个读数（96 Mb数据）中，我们将叶绿体基因组组装成两个重叠群。根据与参考叶绿体基因组进行比较确定的23个多态区域对该杂草稻进行了分类。我们检测了叶绿体和核基因组之间遗传物质转移的最新和过去事件，并估计了它们的发生频率。讨论：我们从低覆盖率的测序数据中获得了高质量的完整叶绿体基因组序列。基因组间DNA转移似乎比以前认为的要频繁。

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